Row

Map with receivers that detected S. acanthias

side row?

Row

Table

---
title: "Squalus acanthias ETN detections overview"
output:
  flexdashboard::flex_dashboard:
    source_code: embed
    orientation: rows
    vertical_layout: scroll
    theme: 
      version: 4
      bootswatch: litera
editor_options: 
  chunk_output_type: console
---

```{r setup, include=FALSE, echo = F}

# knitr::opts_chunk$set(echo = F)
# Sys.setlocale("LC_TIME", "English") # language = English, does not work right now

# fundamentals
library(flexdashboard)
library(etn)
library(knitr)

# data wrangling
library(readr)
# library(tidyverse)
library(lubridate)
library(dplyr)
library(lubridate)
library(utils)
library(forcats)

# maps
library(leaflet)
library(leafem)

# plotting and tables
library(DT) # for interactive tables
library(ggplot2)
library(kableExtra)
library(plotly)
library(scico) #colour palettes

# database connection
con <- etn::connect_to_etn(Sys.getenv("userid"), Sys.getenv("pwd"))
```


```{r database query, include=FALSE, echo=FALSE}


```

<!-- Overview: Receiver stations --> 
<!-- ===================================== -->

Row {data-height=1000}
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### Map with receivers that detected S. acanthias
    
```{r map}
#, include=T, echo=F

# EMODnet Bathymetry layer
# emodnet_tiles <-"https://tiles.emodnet-bathymetry.eu/2020/baselayer/web_mercator/{z}/{x}/{y}.png"
# cite_emodnet <- "<a href='https://emodnet.ec.europa.eu'>EMODnet</a>"
# attr(cite_emodnet, "class") <- c("html", "character")
# 
# # special icons
# # a single icon is declared
# icon_tag <- leaflet::makeAwesomeIcon(
#   icon = "tag",
#   iconColor = "black",
#   markerColor = "yellow",
#   library = "fa"
# )

# colour palettes
# col_fun <- scico::scico(n = stations$deploy_latitude %>% unique() %>% length(),
#                         palette = "roma")
# pal <- leaflet::colorFactor(col_fun, domain = stations$deploy_latitude)
# qpal <- colorQuantile(col_fun, domain = stations$deploy_latitude, n = 5)
# palette_latitudes_df <- tibble(deploy_latitude = stations$deploy_latitude, color = pal(stations$deploy_latitude))
# 
# 
# legend_latitudes <- stations %>% 
#   dplyr::mutate(bin_n5 = deploy_latitude %>% dplyr::ntile(n = 5)) %>%
#   dplyr::group_by(bin_n5) %>%
#   dplyr::summarise(min = deploy_latitude %>% min(),
#                    max = deploy_latitude %>% max()) %>%
#   dplyr::mutate(color = qpal(stations$deploy_latitude) %>% unique())
# 
# leaflet() %>% 
#   
# #background
#   # addTiles() %>%
#   addProviderTiles("Esri.WorldImagery", options = providerTileOptions(opacity = 0.6), group = "satellite") %>%
#   leaflet::addTiles(urlTemplate = emodnet_tiles,
#                     # options = leaflet::tileOptions(tms = FALSE),
#                     attribution = cite_emodnet,
#                     group = "EMODnet bathymetry") %>%
#   # addRasterImage(bathy_belgium_raster, opacity = 1, colors = "Spectral", group = "bathymetry") %>%
#   # addPolygons(data = coastline_BE_poly, opacity = 1, fillColor = "grey", weight = 0, fillOpacity = 0.7, group = "bathymetry") %>% #"#ECE4BF"
#   addTiles(group = "OpenStreetMap") %>%
# 
# #data: receiver stations
#   addCircleMarkers(data = stations,
#                    # clusterOptions = markerClusterOptions(showCoverageOnHover = F, zoomToBoundsOnClick = T, freezeAtZoom = 7),
#                    lat = ~deploy_latitude,
#                    lng = ~deploy_longitude,
#                    radius = 5,
#                    color = "black",
#                    weight = 1,
#                    fillOpacity = 1,
#                    fillColor = ~pal(deploy_latitude),
#                    opacity = 1,
#                    label = ~paste0("station ", station_name),
#                    popup = ~paste0("lat: ", deploy_latitude, ", lon: ", deploy_longitude),
#                    group = "receiver stations"
#                    ) %>%
#   
# #data: tagging locations
#   addAwesomeMarkers(data = tagging_locations,
#                    icon = icon_tag,
#                    clusterOptions = markerClusterOptions(), #showCoverageOnHover = T, zoomToBoundsOnClick = T, 
#                    lat = ~releaseLatitude,
#                    lng = ~releaseLongitude,
#                    # radius = 5,
#                    # fillOpacity = 0.7,
#                    # fillColor = "yellow",
#                    # opacity = 0,
#                    label = ~paste0("name: ", tagging_location),
#                    popup = ~paste0("lat: ", releaseLatitude, ", lon: ", releaseLongitude, ", #sharks tagged: ", ind_tagged),
#                    group = "tagging locations"
#                    ) %>%
# 
# # add-ons
# leaflet.extras::addFullscreenControl() %>%
#   leafem::addMouseCoordinates() %>%
#   addScaleBar(position = "bottomright",
#               options = scaleBarOptions(
#                 maxWidth = 150,
#               imperial = FALSE)) %>%
#   
# # layers control
#   addLayersControl(position = "topright" ,
#                    baseGroups = c("EMODnet bathymetry", "satellite", "OpenStreetMap"),
#                    overlayGroups = c("receiver stations", "tagging locations"),
#                    options = layersControlOptions(collapsed = FALSE)) %>%
#   hideGroup("tagging locations") %>%
#   
# # legend
#   addLegend(position = "bottomleft",
#             colors = legend_latitudes$color %>% rev(),
#             labels = paste0(legend_latitudes$min %>% round(), " - ", legend_latitudes$max %>% round()) %>% rev(),
#             opacity = 1,
#             title = "Latitude")

# MWE

# leaflet() %>%
#   addTiles() %>%
#   addCircleMarkers(data = stations,
#                    lat = ~deploy_latitude,
#                    lng = ~deploy_longitude,
#                    color = ~pal2(deploy_latitude)) %>%
#   addLegend(position = "bottomleft",
#             colors = legend_latitudes$color,
#             labels = paste0(legend_latitudes$min %>% round(), " - ", legend_latitudes$max %>% round()),
#             opacity = 1,
#             title = "Latitude")

```
  
<!-- > Map with receiver deployments and acoustic detections. -->
 
    
### side row?
    
```{r abacus}


```



Row {data-height=1000}
-------------------------------------


### Table 

```{r table}

# DT::datatable(animals %>%
#                 dplyr::select(idPk, catchedDateTime, tagging_location, utcReleaseDateTime, sex, tag, releaseLatitude, releaseLongitude),
#               rownames = F,
#               filter = 'bottom',
#               extension = 'Buttons',options = list(
#                 dom = 'Bfrtip',
#                 buttons = c('pdf', 'csv', 'excel', 'print','copy'),
#                 columnDefs = list(list(className = 'dt-center', targets = '_all'))
#               )
#             )
#           
          # ))
          #     options = list(pageLength = 10, autoWidth = TRUE, columnDefs = list(list(className = 'dt-center', targets = '_all')))
          #     ) 

# %>%
#   formatStyle(
#   c('receiver_id', 'battery_estimated_end_date'),
#   fontWeight = "bold") %>%
#   formatStyle(
#   'needs_battery_change',
#   backgroundColor = styleEqual(c(0, 1), c('#90BF87', '#F9938E')))

```


<!-- Details: Acoustic Projects & Detections -->
<!-- ===================================== -->